iterator interface (v0.3)

Project.toml

@@ -9,9 +9,11 @@ CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+GeneticVariantBase = "2447270c-d849-4bf9-ac0d-b5c0b265991c"
 HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 VariantCallFormat = "28eba6e3-a997-4ad9-87c6-d933b8bca6c1"
 
 [compat]

src/VCFTools.jl

@@ -8,11 +8,13 @@ using DelimitedFiles
 using Dates
 using SpecialFunctions
 using VariantCallFormat
+using GeneticVariantBase
+using GeneticVariantBase: n_samples, n_variants
 import VariantCallFormat.findgenokey
 
 export conformgt_by_id, conformgt_by_pos,
     gtstats, geno_ismissing,
-    nrecords, nsamples, openvcf,
+    nrecords, nsamples, openvcf, VCFData,
     sampleID,
     grm,
     # convert functions
@@ -32,13 +34,15 @@ export conformgt_by_id, conformgt_by_pos,
     write_vcf
 
 # package code goes here
+
 include("gtstats.jl")
 include("conformgt.jl")
 include("convert.jl")
 include("filter.jl")
 include("aim_select.jl")
 include("grm.jl")
 include("write.jl")
+include("iterator.jl")
 
 # test data directory
 datadir(parts...) = joinpath(@__DIR__, "..", "test", parts...)    

src/VCFTools.jl.31574.mem

@@ -0,0 +1,50 @@
+  3534212 module VCFTools
+        - 
+        - using CodecZlib
+        - using Distributions
+        - using HypothesisTests
+        - using ProgressMeter
+        - using DelimitedFiles
+        - using Dates
+        - using SpecialFunctions
+        - using VariantCallFormat
+        - using GeneticVariantBase
+        - import VariantCallFormat.findgenokey
+        - 
+        - export conformgt_by_id, conformgt_by_pos,
+        -     gtstats, geno_ismissing,
+        -     nrecords, nsamples, openvcf,
+        -     n_samples, n_variants,
+        -     sampleID,
+        -     grm,
+        -     # convert functions
+        -     save_snpinfo,
+        -     convert_gt, copy_gt!,
+        -     convert_ht, copy_ht!,
+        -     convert_ds, copy_ds!, 
+        -     copy_gt_trans!, copy_ht_trans!, copy_ds_trans!,
+        -     # filter functions
+        -     filter_genotype, 
+        -     filter, filter_header, 
+        -     filter_chr, filter_range,
+        -     mask_gt, find_duplicate_marker,    
+        -     # aim selection
+        -     aim_select,
+        -     # write routines
+        -     write_vcf
+        - 
+        - # package code goes here
+        - 
+        - include("gtstats.jl")
+        - include("conformgt.jl")
+        - include("convert.jl")
+        - include("filter.jl")
+        - include("aim_select.jl")
+        - include("grm.jl")
+        - include("write.jl")
+        - include("iterator.jl")
+        - 
+        - # test data directory
+        - datadir(parts...) = joinpath(@__DIR__, "..", "test", parts...)    
+        - 
+        - end # module

src/VCFTools.jl.31602.mem

@@ -0,0 +1,50 @@
+  3238747 module VCFTools
+        - 
+        - using CodecZlib
+        - using Distributions
+        - using HypothesisTests
+        - using ProgressMeter
+        - using DelimitedFiles
+        - using Dates
+        - using SpecialFunctions
+        - using VariantCallFormat
+        - using GeneticVariantBase
+        - import VariantCallFormat.findgenokey
+        - 
+        - export conformgt_by_id, conformgt_by_pos,
+        -     gtstats, geno_ismissing,
+        -     nrecords, nsamples, openvcf,
+        -     n_samples, n_variants,
+        -     sampleID,
+        -     grm,
+        -     # convert functions
+        -     save_snpinfo,
+        -     convert_gt, copy_gt!,
+        -     convert_ht, copy_ht!,
+        -     convert_ds, copy_ds!, 
+        -     copy_gt_trans!, copy_ht_trans!, copy_ds_trans!,
+        -     # filter functions
+        -     filter_genotype, 
+        -     filter, filter_header, 
+        -     filter_chr, filter_range,
+        -     mask_gt, find_duplicate_marker,    
+        -     # aim selection
+        -     aim_select,
+        -     # write routines
+        -     write_vcf
+        - 
+        - # package code goes here
+        - 
+        - include("gtstats.jl")
+        - include("conformgt.jl")
+        - include("convert.jl")
+        - include("filter.jl")
+        - include("aim_select.jl")
+        - include("grm.jl")
+        - include("write.jl")
+        - include("iterator.jl")
+        - 
+        - # test data directory
+        - datadir(parts...) = joinpath(@__DIR__, "..", "test", parts...)    
+        - 
+        - end # module

src/VCFTools.jl.31604.mem

@@ -0,0 +1,50 @@
+  3534212 module VCFTools
+        - 
+        - using CodecZlib
+        - using Distributions
+        - using HypothesisTests
+        - using ProgressMeter
+        - using DelimitedFiles
+        - using Dates
+        - using SpecialFunctions
+        - using VariantCallFormat
+        - using GeneticVariantBase
+        - import VariantCallFormat.findgenokey
+        - 
+        - export conformgt_by_id, conformgt_by_pos,
+        -     gtstats, geno_ismissing,
+        -     nrecords, nsamples, openvcf,
+        -     n_samples, n_variants,
+        -     sampleID,
+        -     grm,
+        -     # convert functions
+        -     save_snpinfo,
+        -     convert_gt, copy_gt!,
+        -     convert_ht, copy_ht!,
+        -     convert_ds, copy_ds!, 
+        -     copy_gt_trans!, copy_ht_trans!, copy_ds_trans!,
+        -     # filter functions
+        -     filter_genotype, 
+        -     filter, filter_header, 
+        -     filter_chr, filter_range,
+        -     mask_gt, find_duplicate_marker,    
+        -     # aim selection
+        -     aim_select,
+        -     # write routines
+        -     write_vcf
+        - 
+        - # package code goes here
+        - 
+        - include("gtstats.jl")
+        - include("conformgt.jl")
+        - include("convert.jl")
+        - include("filter.jl")
+        - include("aim_select.jl")
+        - include("grm.jl")
+        - include("write.jl")
+        - include("iterator.jl")
+        - 
+        - # test data directory
+        - datadir(parts...) = joinpath(@__DIR__, "..", "test", parts...)    
+        - 
+        - end # module